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SSRL Headlines Vol. 10, No. 12  June, 2010


Contents of this Issue:

  1. Science Highlight — 3D Imaging of Bone Structure Key to Understanding Bone Health
  2. Science Highlight — Following the pH-dependent Conformational Changes of a Maturing Viral Capsid
  3. Science Highlight — Identifying Novel Targets that Extend the Effectiveness of HIV Protease Inhibitors
  4. Frequent Injection Mode Boosts Resolution for SSRL Users
  5. ZX Shen Becomes Chief Scientist for SLAC
  6. From the Director of Photon Science: A New Initiative in Catalysis and Interfacial Science: Welcome to Prof. Jens Norskov and His Team
  7. Save the Date for the Annual SSRL/LCLS Users' Conference - Oct 17-21, 2010
  8. Call for Nominations for Spicer, Klein and Lytle Awards
  9. Synchrotron Summer School Goes Beyond Textbook Techniques
  10. Dinobird Returns to SSRL
  11. Smoking in Non-designated Smoking Areas is Hazardous to the Site
  12. NUFO Meeting at BNL

1.  Science Highlight — 3D Imaging of Bone Structure Key to Understanding Bone Health
       (contacts: J. Andrews Hayter,; P. Pianetta,

Projection (a) and slices (b and c) from tomography of single bone trabecula imaged from -90 to 90 degrees shows lacuna and canaliculi extending from it.
The 3D structure of bone is critical for maintaining strength. Skeletal diseases such as osteoporosis and environmental conditions such as weightlessness, radiation, and vitamin D deficiency can affect bone structure. Understanding the 3D structure of bone is critical to understanding how these conditions affect bone's form and function.

A team that included scientists from NASA Ames Research Center, Cornell University, Xradia Inc., and SSRL has developed a technique that can be used to image bone structure in 3D at high (30 nanometer) resolution. They used the transmission X ray microscope (TXM) on SSRL Beam Line 6-2 to visualize bone from mice that had undergone a process to simulate weightlessness. Using mathematically reconstructed tomography (nano-CT) images, they created a 3D image of the bone's nanostructures. The scientists were also able to measure bone density on a fine scale.

These techniques can be used to discern the difference between normal and diseased or distressed bone, and responses to treatment. They can also characterize nanoscale changes in bone structures due to weightlessness, and identify differences in subsequent bone regrowth upon weight bearing. This work is of particular interest to NASA because they are interested in the long-term effects of weightlessness on bone density and nanostructure. This work was published in the June issue of Microscopy and Microanalysis.

To learn more about this research see the full scientific highlight

2.  Science Highlight — Following the pH-dependent Conformational Changes of a Maturing Viral Capsid
       (contacts: T. Matsui,; H. Tsuruta,

The capsid that surrounds viruses is formed from subunit proteins that interact in specific ways to form a tight shell. The processes of coming together and forming interactions are multistep and complex and are fundamental events to acquire viral infectivity. The capsid maturation process of the Nudaurelia capensis omega virus includes pH-dependent conformational changes and auto-proteolysis. Like many human viruses such as HIV and herpes virus, NwV, an insect virus, requires these specific structural changes to become infectious.

A group of scientists led by Prof. Jack Johnson of The Scripps Research Institute performed equilibrium and time-resolved small angle x-ray scattering (SAXS) using SSRL Beam Line 4-2 to investigate the properties of NwV capsid maturation. They found that pH-dependent protonation of some of the residues of the capsid proteins allowed them to pack more closely together causing a size reduction of the entire provirion. This quick conformational change, observed in millisecond to second regime, is followed by the slower process of auto-proteolysis taking place over many hours, resulting in the mature structure. Interestingly, capsids exposed to a lower pH did not require a cleavage step to reach the mature structure.

The authors identified three pH-dependent kinetic stages corresponding to capsid compression and strengthening. Their study expands understanding of viral maturation processes. This work was published in the April 7 issue of Biophysical Journal.

To learn more about this research see the full scientific highlight

NwV figure
NwV Maturation

3.  Science Highlight — Identifying Novel Targets that Extend the Effectiveness of HIV Protease Inhibitors
       (contact: C.D. Stout,

Surface rendering of the HIV protease structure showing solvent-exposed clefts on the protein surface into which the fragments bind.
HIV protease is a common and critical drug target for combating HIV infection and AIDS. As HIV develops resistance to anti-viral drugs, new therapies are required. Since most of the virus's mutations that confer drug resistance cluster in the active site of the protease, scientists are interested in molecules that may bind other places on the enzyme. Computer simulations aid the design of drugs and fragments, which are smaller than typical drugs, to bind the enzyme's surface in a way that compliments the activity of traditional active-site binding drugs.

A team of scientists led by Prof. Dave Stout at The Scripps Research Institute has used SSRL beam lines to crystallographically screen fragment binding to HIV protease. They screened 400 fragments and evaluated 800 crystals using SSRL's high-throughput robotic sample automounter system. They found two novel surface-binding sites that induce conformational changes in the protease.

Their study shows that applying this high-throughput method can identify new potential drugs and drug targets that work in combination with existing drug therapies. This may allow current drugs to continue being effective, despite viral mutations. This work was published in the March 2010 issue of Chemical Biology and Drug Design.

To learn more about this research see the full scientific highlight

4.   Frequent Injection Mode Boosts Resolution for SSRL Users
       June 8, 2010 SLAC Today article by Lauren Rugani

SPEAR3 Status Screen
SPEAR3 status screen showing current dropping steadily over each eight-hour cycle prior to the start of frequent injection mode, then became stable around 200 mA beginning at 10:00 a.m. Monday, June 7.
After months of planning and testing, the Stanford Synchrotron Radiation Lightsource began its first user run with the SPEAR3 storage ring operating in frequent injection mode on June 7. This is the most recent in a series of steps toward operating at its full design current of 500 milliamperes, which aims to provide faster and higher resolution data collection for SSRL users.

SSRL began running in what's called top-off mode last year, with the last few beam lines approved for top-off earlier this year. Photon beam lines remained open while electrons were injected into the SPEAR3 storage ring three times a day to replenish the 200-mA current. Still operating in top-off mode, these injections now happen once every 10 minutes, or 144 times a day.

"The number one advantage for operating this way is power constancy," said Tom Rabedeau, who works on beam line development at SSRL. The frequent injections allow the current to remain relatively stable, dropping only about 1.5 mA before more electrons are added. Since the optics used to focus and guide the beams can experience thermal distortion under larger current fluctuations, they perform better under the nearly constant power load provided by the smaller, more frequent injections. Read more at:

5.   ZX Shen Becomes Chief Scientist for SLAC
       Excerpt from June 25, 2010 SLAC Today article by SLAC Director Persis Drell

ZX Shen
ZX Shen
It gives me great pleasure to announce that Professor Zhi-Xun Shen-known to all of you as a professor of physics, applied physics and photon science, and the division director for the Stanford Institute for Materials and Energy Sciences, or SIMES, at SLAC-has agreed to serve as SLAC's chief scientist. In this role, ZX will assist in lab wide strategic planning and direction particularly in the area of basic energy sciences. He will assist SLAC in developing activities in energy research and an energy research strategy, and he will be our primary interface with Stanford in these areas. He will work to facilitate joint appointments with campus departments in connection with the photon science faculty chair and the associate dean. ZX is also taking on the responsibility to grow our energy research portfolio at SLAC. Read more at:

6.   From the Director of Photon Science: A New Initiative in Catalysis and Interfacial Science: Welcome to Prof. Jens Norskov and His Team
       June 8, 2010 SLAC Today article by Keith Hodgson

H. Wellejus, Fr. Abild-Pederson & J. Norskov
from left: Helle Wellejus, Frank Abild-Pedersen and Jens Norskov
In my SLAC Today Director's column on Friday, June 4, I discussed the many changes taking place in the Photon Science Directorate that position the lab for future growth and delivery of science essential for achieving future SLAC and Department of Energy missions. Today I am extremely pleased to announce an exciting next step in realizing those objectives, with the arrival of Jens Norskov and a new initiative in catalysis and interfacial science being developed and led by Jens.

Catalysts are widely used in many industrial processes, including energy production and mitigating pollution. New catalysts also hold the key to future energy technologies such as efficiently splitting water to form hydrogen or other fuels. To design these technologies, we first need to understand how catalysts carry out their function on the atomic level. We currently do not have a unifying predictive strategy (as for example the Standard Model provides for the field of high energy physics). Jens and his team are leading designers of new materials, especially for catalysis and energy storage applications, using advanced techniques of theory, modeling and simulation. Jens' new center at SLAC will provide a unique capability to understand and model new materials which can then be synthesized. Our light sources at SLAC (LCLS and SSRL) offer valuable techniques for characterizing the new materials. These materials can then be tested for improved catalytic properties with the ultimate goal of finding real world applications. Read more at:

See also June 4 SLAC Today article at:

7.   Save the Date for the Annual SSRL/LCLS Users' Conference - Oct 17-21, 2010        (contact: C. Knotts,

Plans are underway for the Annual SSRL/LCLS Users' Meeting and Workshops, October 17-21, 2010. Mark your calendar and plan to participate to learn about new developments and exciting user research at LCLS and SSRL. It is also a great time to interact with other scientists, potential colleagues, and vendors of light source-related products and services. Check back later for more details and registration.

8.   Call for Nominations for Spicer, Klein and Lytle Awards
       (contact: C. Knotts,

Please take a few moments to consider nominating your colleagues or students for one or more of the following awards which will be presented at the Joint SSRL and LCLS Users' Meeting, October 17-21, 2010:

9.   Synchrotron Summer School Goes Beyond Textbook Techniques
       June 8, 2010 SLAC Today article by Julie Karceski

SR School Participants
SRXAS 2010 attendees. (Photo by Nikola Stojanovik)
About 45 researchers gathered at SLAC in early June for the fifth annual Stanford Synchrotron Radiation Lightsource School on Synchrotron X-ray Scattering Techniques in Materials and Environmental Sciences: Theory and Application. This workshop had a simple goal: to familiarize more scientists with synchrotron x-ray diffraction experiments. The participants, who were mostly graduate students and postdocs from nearby schools, spent June 1-3 learning new techniques to probe technological and environmental materials.

"It's a practical, hands-on type of workshop," said co-organizer Mike Toney, a SLAC scientist with SSRL. "What we explained and demonstrated is typically not found in textbooks." A working understanding of the beam lines at SSRL is crucial to successfully studying nano- and atomic-scale structures.

Some of the experimental methods covered include thin-film scattering, powder diffraction, small angle x-ray scattering and x-ray reflectivity. One and one-half days of this workshop were devoted to explanatory talks, one day to gaining hands-on experience at the SSRL beam lines, and the last half day was spent working on data analysis. See:

10.   Dinobird Returns to SSRL       

archaeopteryx at BL6-2
Archaeopteryx Fossil at BL6-2 (Photo by Nikola Stojanovic)
Pete Larson, renowned paleontologist and president of the Black Hills Institute, participated in a webinar through the Houston Museum of Natural Science (HMNS) on June 17 while conducting fluorescence imaging studies at SSRL BL6-2. During the live broadcast, Larson discussed his new research on the Thermopolis Archaeopteryx specimen and answered questions from the press and general public. This research offers insight into the Thermopolis Archaeopteryx fossil, which is one of the best known examples of this species. Thermopolis Archaeopteryx and the other fossils were found in the world-renowned quarries of Solnhofen. Of the 10 Archaeopteryx fossils that are known, only one is on display in North America, in the HMNS exhibit 'Archaeopteryx: Icon of Evolution.' During the webinar, Larson led guests on a video walkthrough of the exhibit, described his most recent studies, and explained why these exquisitely preserved specimens are important to the scientific community. To many scientists and scholars, the species represents the evolutionary gap between dinosaurs and modern day birds.

11.   Smoking in Non-designated Smoking Areas is Hazardous to the Site
       (contact: I. Evans,

Due to the extreme fire danger in Northern California, SLAC policy requires that anyone who smokes on SLAC property do so in specifically designated areas. The policy also requires anyone barbecuing on SLAC property to first obtain a Hot Work Permit. Contact building managers for more information on the designated smoking areas for specific buildings/areas which should include fire-proof disposal containers at least 20 feet from readily combustible or flammable materials. In addition, designated smoking areas need to be at least 20 feet away from any doorway, walkway, air intake or functional window and not in a pathway that a non-smoker must use to enter a building. Furthermore, smoking is expressly prohibited along the Linac Roads, in any area near grasslands, and in SLAC or General Services Administration vehicles. For more information, see

12.   NUFO Meeting at BNL
       (contacts: C. Knotts,; K. Kantardjieff, The annual meeting of the National User Facility Organization (NUFO), held June 7-9, 2010, at Brookhaven National Laboratory, focused on a number of issues of interest to users-among them educational and community outreach approaches, streamlined access processes for non-US citizens, further standardization of user agreements, and industrial use of various user facilities. NUFO represents the interests of users of national user facilities as well as American users of international user facilities. The next meeting will be held at SLAC in 2011. Contact Cathy Knotts, Katherine Kantardjieff, or anyone on the NUFO Steering Committee to suggest discussion topics for the next meeting. To access copies of the presentations from the 2010 meeting or for further information about NUFO activities, visit or e-mail


SSRL Headlines is published electronically monthly to inform SSRL users, sponsors and other interested people about happenings at SSRL. SSRL is a national synchrotron user facility operated by Stanford University for the U.S. Department of Energy Office of Basic Energy Sciences. Additional support for the structural biology program is provided by the DOE Office of Biological and Environmental Research, the NIH National Center for Research Resources and the NIH Institute for General Medical Sciences. Additional information about SSRL and its operation and schedules is available from the SSRL WWW site.


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Last Updated: 30 June 2010
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